<meta charset="utf8">
<title>My marker gene list</title>



<pre>
<h3>详细</h3>
markers=list(
  epithelial=c(#'KRT14', 'KRT17', 'KRT6A', 'KRT5', 
    'EPCAM', 'KRT8', 'KRT18','KRT19',  #'KRT16', 'KRT6B', 'KRT15', 'KRT6C', 'KRTCAP3', 
    #'SFN', 'PROM1', 'ALDH1A1', 
	'CD24'), 
  fibro=c("MME",'FAP', 'PDPN', "VCAN", #'COL1A2', 'DCN', 'COL3A1', 
	'COL6A1'),
  endo =c('PECAM1', 'VWF', 'ENG'),
  
  #myocytes=c('ACTA1', 'ACTN2', 'MYL2', 'MYH2'), 
  
  "T" =c("PTPRC", #'CD2', 'TRAC','CD7', 
		'CD3D', 'CD3E', #'CD3G', 
		'CD4', 'CD8A', 'CD8B', 'SELL',
         'FOXP3', "CTLA4", "CD274", "PRF1", "IFNG", "RUNX3", "ZBTB7B"),
  NK=c('NKG7', 'GNLY', 'GZMA', 'GZMB', "GZMK", "GZMH","GZMM",
  "NCAM1",  'FGFBP2', 'CX3CR1'),
  B = c( 'CD79A', 'CD79B', 'CD19', 'MS4A1', 'VPREB3', 'SLAMF7','BLNK', 'FCRL5'), 
  Plasma=c('IGHG1', 'MZB1', 'SDC1'),
  mono=c('CD14', "FCGR3A"),
  
  macro=c('CD163', 'CD68', 'FCGR2A', 'CSF1R', "SPP1"), 
  M1=c('NOS2', 'IRF5', 'PTGS2'),
  M2=c( 'VSIG4', 'MS4A4A'), #'CD163',
  
  DC=c('ITGAX','CD40', 'CD80', 'CD83', 'CCR7', "IL7R", "LAMP3", "CD1C"),
  pDC=c("FSCN1","CCL19","IDO1", "IDO2", 'LILRA4', 'IRF7', 'IL3RA'), #MZB1
  MHCII=c("HLA-DQA1", "HLA-DQB1", "HLA-DQB2", "CD74"),
  #mast = c('CMA1', 'MS4A2', 'TPSAB1', 'TPSB2', 'CPA3'),
  
  #eryth=c("HBA1",  "HBA2",  "HBB",   "HBD"),
  neu=c("MPO","ELANE",  "LTF","CAMP", "CMTM2","PROK2","FCGR3B"),
  
  #stem=c('CD34', 'KIT', 'SOCS2', 'SOCS1'),
  #cycle=c('MKI67', 'CCND1', 'CCND3', 'CCNE1', 'CCNE2', 'CCNB1', 'CCNB2'),
  #APA =c('NUDT21', "CPSF6", "CSTF2"),
  meta=c("GAPDH", 'ACTB', "SCCPDH")
)

pdf( paste0(outputRoot, keyword, "_05_2.Manual.marker.DotPlot.pdf"), width=26, height=pdf_height)
DotPlot(scObj_2, features = markers, cluster.idents = T, cols=c('lightgrey', "red")) + RotatedAxis()+
  ggtitle(keyword)
dev.off()





<hr>
<h3>简短</h3>
cell_marker.Simple=list(
  "T Cells"= c('PTPRC', 'CD3D', 'CD3E', "CD3G", 'CD8A', "CD8B", "CD4", "IL7R", "FOXP3"),
  "B cells" = c('CD19', 'CD79A', "CD79B", 'MS4A1'),  #[CD20]
  "Plasma cells" = c('IGHG1', 'MZB1', 'SDC1'), #'CD79A'
  "Monocytes and macrophages" = c('CD68', 'CD163', 'CD14'),
  "NK Cells" = c('FGFBP2', 'FCGR3A', 'CX3CR1'),
  "Photoreceptor cells" = c('RCVRN'), 
  "Fibroblasts" = c('FGF7', 'MME'), 
  "Endothelial cells" = c('PECAM1', 'VWF'),
  "epi or tumor" = c('EPCAM', 'KRT19', 'PROM1', 'ALDH1A1', 'CD24')
  #"immune" =c('PTPRC')
  #"epithelial/cancer" = c( 'EPCAM'), 
  #"stromal" =c('MME', 'PECAM1')
)

DotPlot(tmp, features = cell_marker.Simple, cols = c("lightgrey", "red"), cluster.idents = T)+RotatedAxis()





<hr>
# More gene list:
https://gitee.com/dawnEve/bioToolKit/blob/dev/R_scripts/single_script/do_Seurat.script.R

</pre>
